Dealing with it from the inside

I posted this on FB yesterday, but I think the term “panic attack” is kind of a misnomer. When we say “[x] attack” we normally mean “an attack caused by a/an [x]” – a bear attack is caused by a bear, an epileptic attack is caused by epilepsy, a heart attack… well, in the same way that’s kind of a misnomer too. Anyway, a panic attack isn’t like that. It’s not something caused by panic, it’s something that causes panic at inappropriate things or moments. The problem isn’t that I’m panicking over my bills, my work, or my life choices, it’s that there’s something in my head that’s causing me to react to that (or something else) as though I were being attacked by a bear, and that something will find a stimulus to latch on to, no matter how ridiculous it is. There is a core problem, in some but not all cases a medical one, that causes people to respond to things in an inappropriate manner. It’s not their choice to do this, they don’t want to do this, but despite that they still do.

How do I know that? Because last night at work, and just about as soon as I walked into work this morning, I started having the symptoms of a panic attack (for the record, those for me are: elevated heart rate, respiration, sweating in the absence of heat; increased irritability, impatience, aggressiveness and fear response; irrational thoughts and quick, inappropriate responses to external stimuli. Some or all may be present at any given time.). It didn’t start because I walked in to work, I think (because I deal with that stress just fine every day), but it chose that moment to manifest because that’s the earliest point in my day that I deal with any significant amount of stress. So, strictly speaking, it probably started some time before that, and I only noticed it when it found something to latch on to, and that required just the tiniest bit of stress. That’s how it works.

It’s kind of like an autoimmune disorder, in a way. When you have a regular immune response to something, it is scaled appropriately. When your immune system sees a kidney cell,  it says “Hi kidney cell, how ya doing?” When it sees a virion (viral particle), it kicks it out and says “no ticket.” When it sees a whole invading army of bacterial Nazis (yes, for some reason your immune system is Indiana Jones. No, I don’t know why), it sounds the inflammatory alarm bells and sets off a systemic cascade that recruits a whole bunch of white blood cells to help repel the invasion. When you have something like Crohn’s or Lupus or Rheumatoid Arthritis, your immune system responds to seeing something completely normal – a kidney cell, cartilage, or your own intestines – by setting off the alarm bells and trying to repel the invaders. In this way, a panic attack is similar. A panic attack is your brain reacting to perfectly normal things – school, life, work – or nothing at all by going into fight-or-flight mode, releasing adrenaline into your blood and causing you to physically prepare for the bear to come a-clawin’ at your face.

The way I remember learning about it, many reactions in your nervous system do not involve your brain at all. For instance, when you jerk your knee after the doc hits it with the rubber mallet, for instance, that cascade reaction only involves nerve cells in your leg and spinal cord. Most of the time, your heart rhythm is controlled by your heart. I imagine that to varying degrees, most autonomic functions in your body are that way. It feels like that’s happening here, too, in a tail-wagging-the-dog sort of way. Let me elaborate. It feels like there is something in my body or brain which is outside of my conscious control, which is causing adrenaline to be released into my blood. This causes a whole host of automatic responses that mostly encapsulate the symptoms I listed above. The effect on my brain is to encourage hyper-focus on my immediate surroundings, because that’s absolutely the correct response in a genuine situation where you ought to panic. So, the brain searches for the ‘source’ of the panic, the bear or whatever, and works to eliminate it or remove the situation in some other way. That means that any tiny situation which seems vaguely stressful can become this huge looming thing, simply because your brain decides to latch on to it and make it your whole world for the time being so that you can hyper-focus on it, solve it, and stop the alarm bells. In a normal situation, that would be the best response.

In this situation, that’s a problem. Because there is some persistent, invisible issue at hand, none of the proposed solutions work. Your brain, making a most reasonable assumption, assumes that the thing that it thought was the source of the problem was not. It goes looking for a new source, and the process repeats itself. This results in you panicking about small, meaningless situations and problems-that-aren’t; hyper-focusing on things you can’t address, like bills or why you chose the major you did in college; and just generally being jumpy, irritable, and acting as though every little problem is the end of the world. So in that way, it’s not an attack by panic, it’s an attack that causes panic at inappropriate times or for inappropriate reasons.

Hm. I’ll have to think about this some more. I’ll try to remain calm while I do, and deal with this from the inside.

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Charting a Better Path

America has a strained, sometimes strange relationship with science. When science (or scientific findings, at any rate) vindicates what it already roundly believed to be true it is accepted, lauded, and embraced. When those same findings challenge deeply-held beliefs, desires or predilections, that same science is – sometimes the very same scientists are – very swiftly cast aside or turned into a rhetorical pincushion, an example of intellectual elites in an ivory tower who’ve lost touch with the common man. This strand of American anti-intellectualism has been so well studied as to border on cliche, so rather than examining it in detail I’m going to move on. It’s mostly irrelevant to my eventual point, anyway.

Well, I’m an elite. I’m a scientist. I’ve been in the ivory tower, and have done plenty of biological, chemical and genetic research. At this very moment, I’m sitting in a lab working up exactly how much Benzene is in the municipal drinking water of various localities, maybe even yours (hint: basically none, in all probability). I think, even though sometimes people don’t trust science or scientists, that it is still one of the most effective tools we have at making our world a measurably better place, when combined with good policy and unselfish motivations. So lets give it that policy framework and those motivations, I say.

Basically everyone is agreed that the Earth is pretty swell. We live here, and we like taking care of it. We plant trees, we try not to make a mess, and whenever possible we try to find and make better the good things about this pale blue dot we call home. While we may not always (and in fact almost never) all agree as to how, we can at least start with that common ground as out final aspiration and work out from there.

Specifically today, I’d like to talk about food. The way we produce food, in the United States especially, is in many ways really bad. For us, for the environment, for the rest of humanity, it’s just bad. No, not that we make too many GMO crops or not enough organics, or too few GMOs and too many organics. Although I do have an opinion on that, I understand that that’s a controversial issue that is best tackled when we’ve plenty of time to spare on exhausting debates. We don’t have that kind of time today, or at least I am disinclined to having that particular debate right now. No, what I mean is that we use too much fertilizer (organic and conventional farms both do this), we use too much pesticide (organic and conventional farms both do this), we use too many fossil fuels transporting out food halfway round the world, and we produce too much food that too few people can afford (organic and conventional farms both do this), and we have successfully made unprofitable the farming practices that allowed farmers to be responsible stewards of the land for generations (again, organic and conventional farms both do this). That’s turning farming into the province of Agribusiness, of Monsanto. That is a bad thing, for people and the environment, for producers and consumers.

First of all, we need to recognize that farmers fundamentally want to care for the land. The land is their legacy, and is the inheritance they pass on to their children. We need to enable them to be the stewards they want to be, instead of structuring our laws so that they are encouraged to farm in a way that is, over the long-term, unsustainable. Also, we need to structure our laws so that they encourage and enable small farmers to prosper, so that farming doesn’t become the province of mega-corporations who have no inherent interest in environmental stewardship, sustainability, or the common good.

Next, we need to recognize that our good intentions sometimes have really devastating consequences. For instance, you’d think that providing food aid (to Africa, for instance) would be a no-brainer. People are hungry so feed them, right? Unfortunately, as good as those intentions are, it doesn’t quite work out that way. By flying tons of food over to countries who just need a little temporary help, we depress the prices of food in those countries and make it impossible for the farmers there to make a profit. As a result, they are driven out of business. When a country has no farmers of its own other than subsistence farmers, it can’t ever stop being helped with food aid from abroad. Also, it turns out that the fuel cost to fly food around the world is immense. It would be much cheaper in the long run if we could instead spur the growth of local food production, instead of relying on our own food and flying it halfway round the world.

Next, we need to recognize that while we may not have a common preferred means to achieve the goal of sustainable food production, we do have that goal in common no matter where we are or who we are talking to. Very few people indeed want unsustainable agriculture. So instead of focusing in particular on how we get there, just set our destination as a common end point and reward those who get farther along on that path. That way, no matter who ends up being right – GMOs,/GE crops organics, heirlooms, holistic farming, permaculture, polyculture, etc – we’ll have still gotten farther along that path. So no matter who ‘wins,’ we all win in the end. I think we can all agree that that’s a good thing.

But how do we do it? Well, my ideas aren’t perfect, and aren’t an ideal solution, but here are a few of them.

Restructuring farm subsidies:

Currently in the United States, we essentially pay farmers a certain minimum income per acre per year, up to a certain maximum value, regardless of the amount of crops they produce. However, we subsidize crops at different rates per acre depending on what is grown. Unsurprisingly then, farmers tend to plant what the government subsidizes at the highest rate in order to earn the most they can per acre of crops. Then, they plant the same thing next year, and the year after, and the year after, fertilizing the land with synthetic fertilizers as necessary in order to maintain productivity. For the same reason, they use pesticides as much as they need to, to combat the ever-growing number of insects that prey on their crops.

What I’d like to see is that instead of paying farmers a variable amount for the crops they produce, pay them a subsidy based upon producing what we need. In order to see to that, I propose that we create a panel in the Dept. of Agriculture that would be tasked with setting a target each year for the number of tons of each major crop that American farms ought to produce. Then, pay farmers to meet that target. Rely on things like food processors and lobbyists to communicate with this body the needs of those they represent, and have them then use that knowledge to get us to where we need to be. In addition, use farm subsidies to encourage Best Practices in agriculture. For instance –

* Increase the per acre subsidy by 5-10% if a farmer plants a different thing on that acre this year than he planted there last year (crop rotation)

* Increase the per acre subsidy by 5-10% if a farmer uses substantially less pesticide than is typical

* Increase the per acre subsidy by 5-10% if a farmer uses substantially less fertilizer than is typical

* Increase the per acre subsidy by 5-10% if a farmer produces at least three to five different crops in their fields

* Decrease the per acre subsidy by 10-20% if the farm is owned by a corporation worth more than, say, $20 million

Restructuring Food Aid:

One of the other areas that we need to reform is the way we provide food aid to the developing world. Currently, what we do is simple. When a place demonstrates a need for it, we fly food over to that place and distribute it, generally free of charge. While this helps solve the immediate problem of starvation in those areas, it drives local farmers out of business. In so doing, it locks those countries into a cycle of dependency on foreign food aid. Rather than allow that, we need to find a better way to help people when they need help, but also help them to in the long term help themselves.

What I’d like to see is that any time we activate our food aid program, we then appropriate a dollar amount to that program equivalent to the number of tons of food we intend to disburse, according to the local market price of that food. Then, we go into the country and buy their entire crop of food at the market price plus 5%, and whatever money we have left over we instead devote to flying food aid to that country, up to a maximum number of tons that is equated with the needs of that country. Then next year, we do the same thing, and keep doing it until local production is such that we are no longer sending them food aid. At that point their own domestic production will be self-sustaining, and they will no longer need our help.

Those are my initial thoughts. What are yours?

Genetic Engineering in our Daily Lives (pt. 2)

In the last installment, we discussed the history of genetic engineering and how we got from the discovery of DNA’s structure to approximately 1980. The focus of this installment will be to get us to the present moment, and in so doing to shed some light on and thereby demystify the process of making genetically engineered organisms somewhat. This isn’t meant to provide you with the technical understanding required to do genetic engineering yourself – that is the focus of some peoples’ whole careers – but to help you to in general terms understand what goes into foods or other items that have been genetically engineered, how they are different from their un-engineered counterparts, and also to provide you with a framework to understand the complexities that are inherent in some of the issues that surround regulating genetically engineered organisms in our foods, medicine, and so on.

Vocabulary of Genetic Engineering

Just like last installment began with a discussion of GE and GMO and why it is important to distinguish between the two, we need to start now with discussing some vocabulary. Unlike last time, I just need to familiarize you with some terms, because I can’t really avoid using them and keep true to my subject matter. This glossary assumes a high school level understanding of Biology; if that’s not where you’re at, feel free to ask for clarification and I will endeavor to provide it.

  • DNA, RNA and Protein: These are the three basic steps in what is called the “Central Dogma” of molecular biology, or the three steps in the normal transition of genetic information into functional information. It normally works that DNA is kind of like a cell’s 4D blueprints, kept behind protective barriers inside the nucleus so that it wont be altered, because in the DNA is stored the final information on all (or much of) of a cell’s inherent programming. That inherent information is then translated into a an RNA-based “working copy,” and then that is translated into a protein. Protein is the actual actor in this process, normally; all of the other steps are just there for quality control, basically. This is all oversimplified, also, but that is the basic overview of the process.
  • cis- and trans-genic: We see these prefixes thrown about in all sorts of settings, these days. They got their start, for the most part, in chemistry. In that context, cis- meant “on the same side of the molecule [as each other]” and trans- meant “on the opposite side of the molecule [from each other]”. In molecular biology, they are used a little differently. They are, rather than descriptions of chemical structure, instead a description of two major types of genetic engineering. Cis-genic engineering is the engineered alteration of an organism by adding DNA from another population with which that organism can normally interbreed – so, adding wheat DNA to wheat, corn DNA to corn, fruitfly DNA to fruitflies, and so on. Trans-genic engineering is the engineered alteration of an organism by adding DNA from some other organism the source cannot normally breed with – so, adding jellyfish DNA to tuna, or fish DNA to tomatoes, or bacterial DNA to plants.
  • Replication, Transcription, Translation: These are three cellular processes that are very important to genetic engineering. Replication is the process that DNA undergoes in order to reproduce accurately and be sorted into daughter cells. Transcription is the process whereby DNA is turned into readable RNA, often with the intent to turn that RNA into protein. Translation is the last step, the use of an RNA template to drive the creation of a protein with a defined sequence and structure. We name these differently because, although they sound quite similar, they are in fact completely distinct processes in the cell that are each incredibly complicated.
  • Promoters, Enhancers, and Inhibitors: These are three major kinds of genetic sequences that govern transcription. The first of the three directs your cell to transcribe the DNA next to it, at a specific time and under a specific condition. This direction can be as general as “all the time, everywhere” to “in between 8 and 14 years of age inside the pituitary gland” or “whenever I eat lots of sugar”. The second of the three, Enhancers, are basically there to amplify transcription at a certain place and time. Promoters establish an on/off level of transcription, called a “basal” level, where Enhancers tweak that by as much as 100- or 1000-fold in a given place, at a given time. Inhibitors do the opposite. They turn off or turn down the transcription of a certain gene at a certain time/place/condition, either back to the basal level or off entirely.
  • mRNA, tRNA, rRNA, and ds/ssRNA: RNA is a funny critter. It plays many different roles in the cell, which means that it basically plays some part in every role in the transition between DNA and protein. mRNA (messenger RNA) is the “working copy” mentioned earlier, it carries the actual genetic information that is then turned into a protein. rRNA  (ribosomal RNA) is part of the scaffolding on the cellular machinery that drives translation, which is also made up of quite a bit of protein. tRNA (transfer RNA) is the carrier and gatekeeper for the building blocks that make up your proteins, and it is tRNA that does the grunt work of making sure that the right amino acids are inserted in the right sequence into the growing chain that is a protein. The last two kinds, “ds” and “ss” are chemical categories, being abbreviations of “double stranded” and “single stranded”. All normal, working RNA in your body is single stranded; if RNA is ever bonded into a double stranded state, your body basically recognizes it as broken and breaks it down to its constituent nucleotides on the spot, to reclaim the spare parts that would otherwise be wasted.

Glossary of Genetic Engineering Schemes

Rather than go through each of the hundreds of kinds of genetically engineered organisms out there, I’m going to focus on giving you a basic understanding of the various schemes and strategies used in genetic engineering and how they each affect the organism, so that you can more faithfully analyze and more completely understand what it is you’re looking at, when you’re reading an article about genetically modified corn or rice or sugar beets, later on.

Classical trans-genic engineering

This is what most people think of, when they think of genetic engineering. Classical trans-genic engineering is the addition to an organism of trans-genic DNA – so, the addition of something like the DNA of a jellyfish into the DNA of a rice plant. This has been used most often to move resistance traits – genes that confer resistance to things like drought, heat, Roundup, or infestation by certain insects – from one plant to another, so that you can easily and (relatively) swiftly make a plant that is both nutritious and resistant to certain herbicides, or that is both fast-growing and resistant to certain diseases like blight or wheat rust. It is done by taking an entire gene (which includes the part that is translated, a part that tells it when and where to turn on, and usually a couple of parts that helped the gene be moved by the scientists in the first place) out of a host organism, putting it into a mechanism of some kind (the mechanism varies with the organism), and using that mechanism to insert it whole-cloth into the target organism. Sometimes this has to be done several times, in order to insert “helper” genes that improve the function of the primary gene, or to transfer additional traits to the target organism.

Once the DNA has been inserted into the target genome and the target has reproduced a few times, the inserted DNA is chemically indistinguishable from the target’s own DNA. That is because, for all intents and purposes, it is the target’s own DNA.

Regulation of transcription

Sometimes, one doesn’t want to add something new to an organism, but just to get rid of something that’s already there or to make it more/less prominent. Usually, this is done by regulating how often and at what time transcription of a given gene occurs. You can do this by replacing a gene’s promoter, by altering how its enhancer interacts with it, or by allowing an inhibitor to either work or not work on it. Only rarely do these alterations involve the addition of transgenic DNA, since the cell wouldn’t recognize that anyway; they usually involve the alteration, substitution, addition or deletion of existing elements, the effect of which is to simply change how the pieces that make up an organism interact with each other.

Regulatory elements are usually fairly specific to the organism and its close genetic relatives, in the same genus or taxonomic family. So, in altering something that occurs in wheat, you almost never need to do anything that could ever affect the transcription of any other genes of any other organisms, anywhere.

Regulation of translation

Another step in the process where engineering can be targeted is translation. In controlling how and when a gene becomes a protein, a gene’s effect can be very precisely controlled, so that in certain places and times its effect is increased while in others it is diminished or negated entirely. This is also often called by another name – RNAi, or RNA interference – because one kind of translational regulation involves inserting a nonsense gene into an organism, which will affect the way a target gene is translated. This works because RNA, if paired with some other strand whose sequence is its mirror image, will bond to it and end up being double stranded much like DNA. Unlike DNA, though, when RNA becomes double stranded it essentially becomes useless. Cells have the ability to identify dsRNA, and thereafter to degrade it without translating it, seeing to it that the original gene never becomes a protein in the first place.

When performing RNAi, nonsense genes are inserted into a target genome. These nonsense genes do not and cannot become genes themselves, as they lack the sequences to kick start the machinery of translation, and so the only thing they are capable of doing is bonding to their complementary not-nonsense target gene, and inhibit its function.

Cis-genic engineering

Finally, more recently a form of genetic engineering that uses genes from other members of the same species has come into prominence. This essentially speeds up the natural processes of cross-breeding, and targets it to a specific purpose, by using the organisms own genes to give it some property or trait that it didn’t have before. This is easier and more directed than selective breeding, because through other molecular biological procedure we can assess whether the transformation was a success and to what extent, without needing to go through several generations of growth to check for the inclusion of dangerous, deleterious recessive genes.

Popular varieties of genetically engineered organisms

Genetically engineered products have a profound place in our daily lives. When we think of “GMOs” (or, as discussed earlier, the more appropriately named “GEOs”) we think of food, but it doesn’t nearly stop there, and it’s not limited to just the varieties covered in popular media or on the internet. This section is devoted to dispelling that misunderstanding, by rounding up examples of the most popular, widespread kinds of GEOs and a few types that, though uncommon are indicative of some important process or principle.

Genetically Engineered Crops

There are myriad varieties of genetically engineered foods, but most are just variations on a few basic themes. A few are unique, in either what they are intended to do or how they do it. The themes are the variations are:

  • Insect-resistant crops (“Bt” or “killer” crops): One of the two most common types of genetically engineered crops, engineering for insect resistance is one of the most effective and widely utilized forms of engineering on the market today. It relies on a natural toxin produced by a bacterium, Bacillus thuringensis, which kills many insects when it is consumed by them and thereby protects the plant into which it has been engineered from persistent colonization by that insect. This same insecticide, in another life, plays a very different role. When simply sprayed over crops and not engineered to be produced within their cells, it is one of the most common organic pesticides in use today. It is engineered into plants by using transgenic methods, as discussed above.
  • Herbicide-resistant crops (RoundupReady, etc): The other most common kind of crop is one that is resistant to herbicides. That on the surface seems rather counter-intuitive, but the reason is quite simple. When one grows grains of pretty much any kind, the most common weed that grows alongside them and thereby impedes their growth is the wild variety of that same grain, which is usually a form of parasitic grass. This is true of corn, wheat, rice, oats, and other crop species. Herbicides like Roundup (a glyphosate-based herbicide) normally kill both the crop and the weed, so they have to be sprayed carefully around the edges of a field or replaced with other herbicides that do the job but are usually much more toxic and much less effective. By making the crop resistant to glyphosate, a farmer can use that herbicide on his crops without fear of damaging them. The gene for glyphosate resistance comes from a soil bacterium called Agrobacterium sp. strain CD4, and is introduced into crop genomes using normal transgenic methods.
  • Disease-, Drought-, Cold- and Heat-Resistant crops: Another few common kinds of crops are those that have been made resistant to some naturally-occurring condition or disease. These are usually made resistant by first identifying the exact protein that the disease or condition affects first, and then finding an alternate form that is resistant. A good example of this is that of a drought-resistant rice, which was developed by splicing a gene called Deep Rooting into a commonly cultivated variety of rice used throughout Asia. Other examples include a blight resistant potato variety, a fungus resistant wheat variety, and variety of corn that is resistant to persistently dry conditions. The gene, which comes from a different, wild variety causes the rice plants roots to grow deep and straight down, as opposed to shallowly outward as they normally do. These are developed by numerous different techniques, some of them cisgenic and others transgenic in nature.
  • Yield Size and Crop Nutrition Improvements: Finally, there are those varieties of crops that are altered in order to simply improve either the quality or the quantity of the crops of edible fruits or grains that are harvested from the crop. These come in a number of specific forms, from Flavr Savr tomatoes that lose flavor more slowly by using RNAi techniques, to rice varieties that improve yield by growing shorter stalks and larger heads of grain, to the much talked about Golden Rice that uses genes from the daffodil and from a soil bacterium in order to produce beta-carotene and thereby helps prevent malnutrition in the third world.
  • Outcrossing and Breeding Control Mechanisms: This final class of biotech merits a mention, but this also comes with a special note. In the 1990s, this kind of crop – called a “terminator” crop – was under development, but due to public outcry it was never finalized or released for public consumption. These varieties are meant to deal with one hypothetical problem identified by environmental advocates – that is, they were worried that transgenes present in engineered crops would be bred into the wild type neighbors of those crops and render them inadvertently transgenic. Even though this concern has been shown to be only hypothetical, multiple companies including Monsanto and Dow developed crop varieties that were unable to produce viable pollen or seeds except in the lab, thereby rendering it incapable of outcrossing. This would have legitimately burdened third world farmers who would not be able to replant any of their cultivated seed from year to year, however, and so development on this variety was stopped before licensing was even sought for its public cultivation.

Genetically Engineered Medicines

One other common reason we employ genetic engineering is to produce medicines. Previously, when a protein or some other gene product is found to be a useful medicine, large varieties of the source organism would then have to be cultivated in order to extract the medicine from them. Eventually, we learned that we could often use bacteria or yeast to do that grunt work more cheaply, more ethically, and more effectively, by programming the aforementioned micro-organisms to produce what we wanted and then cultivating them instead. Some common medicines that we produce in this manner include insulin (previously extracted from horses), follistim (a fertility drug), albumin (used as a safe filler in a number of medications), antibodies, and vaccines. Instead of breeding whole, infectious viruses and then attenuating them with heat or chemicals, which is a faulty process that sometimes results in inadvertent infection, we can use genetic engineering to create a vaccine that contains only a small, non-infectious part of the virus and none of its infectious DNA/RNA, so that it provokes an immune response and thereby confers immunity but has absolutely no risk of infection.

Genetically Engineered Animals

Another growing area of research has been in the creation of genetically engineered varieties of animal. Leaving aside the countless varieties of engineered organism that are created for research purposes (such as fruit flies that are modified in a particular way, or mice that are modified in a particular way), there are a few varieties that have been created as an end product, meant for final use in their modified state. None of those varieties have been subjected to the process for being approved for human consumption, so there is no such thing as genetically engineered meat or milk or fish in our food supply right now, but they have been developed for other purposes. A variety of mosquito has been developed that can only successfully breed under peculiar laboratory conditions, and will soon be used to fight Malaria (and other insect-borne diseases). A variety of fish has been developed that uses the presence or absence of a visible glow to advertise whether water is clean, so that it is easier for environmental scientists to rapidly detect toxins in the water supply. More varieties of genetically engineered animal are under development, or are being researched with a mind for further development in coming years. Mostly, this is for the same reasons we develop any other GEO – because someone or everyone finds it useful. A tsetse fly that kills other tsetse flies and stops the spread of Sleeping Sickness, a mosquito that fights Malaria, a fish that fights water pollution, all are attractive prospects because they all benefit the public good, in addition to any varieties which might be developed for profit-making or other commercial purposes.

All of this leads us to part 3, The Controversy, which will be released soon. But in order to truly understand that, you needed to have all of this background material. I hope you’ve understood everything up to this point, but if at any point I’ve been unclear please ask for additional information or clarification and I;ll do my best to help. Thanks!

Genetic Engineering in our Daily Lives (pt. 1)

In the past two years or so, genetic engineering has entered the spotlight of the common cultural discourse. As a result, there has been an explosion of bad information, intentional misinformation, ignorance, and by consequence, fear. As a geneticist by training, this bothers me a great deal. I’ve posted about it before, and I’m sure I’ll do so again, but for my first “Science” post I’d like to do it now.

“GE” versus “GMO”

Before I get to the meat of the matter, we need to talk terminology for a bit. You’ll find that throughout this post and elsewhere, I tend to use “GE” or “Genetically Engineered” rather than “GMO” or “Genetically Modified Organism.” That’s not an attempt to distract or obfuscate; much the opposite, in fact. I use the former term rather than the latter because it is more accurate.

Ever since the beginning of agriculture in Mesopotamia about 10,000 years ago, we’ve been modifying DNA. Ever since we intentionally domesticated the dog, we’ve been modifying DNA. To make those changes, to make fruits get bigger or bodies get smaller, we bred organisms with traits we wanted with other organisms that also had traits we wanted – selective breeding. Another term for this is evolution by artificial selection. In so doing, for instance, we increased the amount of DNA in the strawberry up to 32-fold, so that commercial domesticated strawberries have up to 32 times as much DNA per cell as the wild strawberry, through the duplication of whole chromosomes. In dogs, the changes are more subtle but no less substantial. Genes, and more often regulatory elements – which are stretches of DNA that do nothing other than tell cellular machinery when, where, and how much of a certain protein to make – were changed out, the end result is a creature tailor made for hunting, herding, guarding, or whatever else we desired. The short version of the story is that we have been modifying DNA for a very, very long time.

Engineering is a more intentional, more directed process. When we engineer items, we build things like circuits or rockets or skyscrapers, from nuts and bolts to blueprints and floor plans. We’ve understood the basic structure and importance of DNA for generation or three. Dr. James Watson and Dr. Francis Crick published their landmark paper on the structure of DNA in 1953, and in 1972 we made the first intentional change to living DNA by inserting a gene from one bacterium into another bacterium, proving that it could be done and was stable even after several generations. The process has gotten a whole lot easier and a whole lot more robust since then, but the fundamentals remain largely the same.

Given that it is the latter process that most people are referring to when they use the term “GMO” and not the former process, I choose to use “GE” or “Genetically Engineered” when talking about that, and you should too. If you want to be taken seriously when speaking on scientific issues, start by sounding like you know what you’re talking about.

The Story of Genetic Engineering

It is useful to start our tale with a historical perspective, an exposition on just what genetic engineering is, how it works, and how it came about. Like I mentioned earlier, in 1953 Watson & Crick published their paper on the structure of DNA. That ended one era of scientific inquiry, and started another. Up to that point, the main thrust of research in that field had mostly been directed to determine what the “heritable material” was – or, what was it that was passed on from parent to child that made the latter look and act mostly like a blend of the former (separately and much earlier, scientists [namely Gregor Mendel] had determined how inheritance worked in general, and gave us a basic vocabulary for genetics, but I’m going to ignore that for the moment). They determined that the heritable material was DNA, and then started to work at discovering just what DNA was and how it worked. Through a series of experiments they uncovered the following facts:

  • DNA was a polymer, a molecule made up of building blocks. Those building blocks were Adenine, Cytosine, Guanine, and Thymine. These four molecules were acidic, and were found mostly in the nucleus of cells, so they were called nucleic acids.
  • In any given DNA molecule, there was always exactly as much Adenine as Thymine, and exactly as much Cytosine as Guanine. That ratio was not true for any other pair of nucleic acids.
  • DNA did not come in single molecules, but in pairs. This pairing was joined together by a kind of bond called a hydrogen bond that could break and reform rather easily.
  • DNA was a molecule that, when bonded in stable pairs as happens in regular cells, looked kind of like a twisted ladder. This is called a double helix.

These were all really cool factoids on their own, but until Watson & Crick (and Franklin and Wilkins) synthesized them into a coherent model by adding a few bits of their own data and spending many hours essentially playing with Legos, they were all mildly cool, but not really useful for anything. Then, they published their paper in 1953, and the whole world of molecular biology was set alight with new purpose, and a new era of research began.

After Watson & Crick, the main thrust of genetic and molecular biological research shifted from what the heritable principle was and how it worked, to how we could use it to best benefit society. One of the most important things to happen after that point was a very fortuitous cup of coffee between two scientists – Dr. Herbert Boyer and Dr. Stanley Cohen. They discovered that though they were working on two different topics, their work was very complementary to one another. One was working on plasmids, which were special molecules – chromosomes – that sometimes happened in bacteria, researching how they worked and how they might be made. The other was working on a peculiar defense mechanism in bacteria, called a restriction enzyme. These were proteins that were programmed to cut any DNA that had a particular sequence in it. The sequence was usually uncommon enough that it never occurred in the bacterium’s own DNA, but it did occur in the DNA of other bacteria or viruses that the bacterium was protecting itself against. So, if the bacterium ever encountered any of those bacteria/viruses, the restriction enzymes would cut up the DNA of the target and kill them. But, importantly, the ends of the pieces of DNA that the enzymes cut were “sticky” to other ends of other pieces of DNA cut by the same enzyme. Upon realizing this, a light bulb went off somewhere. If two pieces of DNA – one being the place you wanted to stick a piece of DNA, the other being the piece of DNA you wanted to stick there – were both cut with the same restriction enzyme, you could use one piece of cut DNA like a bandage on the other, and would at once repair the damage and insert the DNA you wanted into the target you wanted.

At first, this was only tried with the DNA of bacteria. Eventually, scientists found that you could mix the DNA of literally anything with anything, at least most of the time, and get the gene you wanted inserted into the DNA you wanted if you did it just right. Out of this discovery was born a whole industry, and hundreds of scientists dedicated their lives to studying this further. I’m one of them, though I must admit my own contributions have been small and unimportant by comparison.

Around this time, people figured out that there was a great deal of money to be made in this. What began as a line of research meant for the public good, to do things like cure cystic fibrosis and sickle-cell anemia, Alzheimer’s and cancer, world hunger and environmental ruin, was turned into an engine of profit for companies like Dow and Monsanto.

In the next page of this history, I’ll cover current applications of genetic engineering along with descriptions and a few details on each. That will lead us into part 3, where I will talk about the current controversy over GE crops.

Continued in part 2…

A Beginning

This is the start of something – hopefully, something that will last a while. It is (rather obviously) my blog. It is not about one thing, but many things, because my life is not about one thing nor am I interested in just one thing. Everything from politics to geekery to science to journalism to my own personal journey with some rough topics is going to be covered. Before I get to that, though, I want to tell you some things about me and about this blog that will help you to understand what’s going to come later.

About this blog

As implied by the title and stated by the tagline and as already stated by me a couple of times now, this blog is not just about one thing. The things it is about are broken into a few categories, which are listed below. Posts will probably come every few days, sometimes more sometimes less. I will endeavor to split the posts into a couple of types. Opinions and comments are just that – my opinions or comments on issues, unsourced and unvarnished, though I will endeavor to make them valuable, thoughtful, and meaningful to you as best I can. You are free to disagree, with either my views or with whether I’ve achieved my goals in presenting them to you. I welcome disagreement, and I’m never absolutely sure of anything, so as long as you’re not just trolling I welcome opinions and comments on my opinions and comments. That’s what the internet is about, after all. Articles are researched, sourced analyses of some topic of particular importance, written after the fashion of the articles I’m used to reading (as I cover below, my education is as a molecular biologist). I’m going to go out of my way to use plenty of sources and to use them in such a manner that you can check them out for yourself whenever possible, and so say so when it is not. In exchange for that, I ask that you read my writing with an open mind, check my sources, and if you still disagree then to speak to the evidence or address its shortcomings in your disagreement. Finally, analyses are detailed looks at one or a small number of items, such as a news story or article on some other site or blog or something. They obviously have at least one primary source, the one upon which I’m making my analysis and which will always be linked if possible, but may have more if I feel it necessary to make my point. So, that said, the main topics of this blog are as follows:

  • Politics: I am interested in a number of political topics, and those topics will probably make up a substantial number of posts on this blog. They aren’t restricted to any one area, since I have about equal interest in economic issues as pro-democracy reform as foreign affairs as  other areas. I’ll talk about them all as the fancy suits me, and try to keep the screaming to a minimum. I really don’t like screaming, and I’m tired of it dominating American political discourse. I’d like to do what I can to change that, however small or practically nonexistent the change ends up being.
  • Geekery: I’ve been a geek for a long time. I started playing Advanced Dungeons & Dragons when I was 8 years old, and have been ever since. I started video games on the likes of Kings Quest, Zelda, Sonic the Hedgehog, Mortal Kombat, Doom, and others. Right now, I only really play a few – World of Warcraft and Guild Wars II being chief among them. I still play Dungeons & Dragons, now in its 4th edition, and run it as well. I’m developing a role-playing game of my own, and am hopefully soon to start playing in Dystopia Rising. So as far as nerd culture goes, I’m pretty deeply embedded. I hope you’ll enjoy sharing my view from time to time.
  • Science: As I said a minute ago, my primary training is in molecular biology. I went into that field because I’m interested in science, because the living world fascinates me, and because I think that science will, already has, and continues to save the world. Because of that, from time to time I will share science that I find really neat, or will cover some topic that is widely misunderstood. This could be GMOs or particle physics or evolution or something else; whatever it is, I’m going to try to cover it in a tone meant for non-scientists, that explains, educates, and helps you appreciate just why I think that thing is just so darn cool. It also might be worth mentioning here that two or three jobs ago, I taught Biology and Physical Science for the Jefferson Parish Public School System.
  • Media: While I find science damn cool, I find science reporting to often be far less cool. It is uninformed, uninformative, and sometimes downright wrong. Other kinds of reporting are no better, often times. Occasionally I will find something worth sharing as-is, but it seems lately that more often than not a popular story needs a rider or some contextual or clarifying information alongside it in order to truly understand what’s going on. These posts will focus on doing just that, on analyzing and improving on and pointing out articles that are either just plan right or just plain wrong. I’ll try to keep it fairly limited, though, because you really could go on forever with analyzing the constant stream of words produced by the media.
  • Religion: In America, religion is part of public life. It touches our every day lives and affects things from public policy and law to foreign relations to Thanksgiving dinner. This widespread impact, and my own unique perspective on religion will frame the handful of posts I have on this topic. I don’t talk about it very much in comparison to the last few topics, but it will probably be mentioned and it certainly is, for the reasons noted above, worth mentioning from time to time.
  • Recovery: A little less than two years ago as of this writing, I was diagnosed with a kind of brain tumor called an acoustic neuroma (or alternately, a schwannoma). It had made me deaf in my right ear, and subsequently caused a host of other symptoms. Its removal caused some more side effects, including the temporary inability to walk, talk, eat, or move the right half of my face. Posts on this topic will be personal tales and comments on my recovery from this, dealing with the remnant symptoms and therapy and such.
  • Louisiana: I live in Baton Rouge, Louisiana. Some posts will be about life and issues centered on the city or the state, local politics or religion or any of the other categories listed above. In that respect it is really a meta-category, encompassing all of the other categories within it.

About me

In order for you to understand where I’m coming from on any of the above, it would help you to know a bit about me. I’m going to keep this fairly short though, so that you’re not just inundated with information about me.

I’m Luke, a 30 year old lab analyst from Baton Rouge, Louisiana. My views on politics are downright progressive, much more so than you’d think from where I live. I am also a Buddhist, waffling between a couple of different varieties and mostly in solitary practice. My training is primarily in molecular biology and genetics, and I’ve previously worked both in academic research about genetic regulation and in industry doing work on environmental and industrial analytical chemistry. My posts all come from that bias, and you should consider that in reading them, but those basic elements are just a short-hand as my particular views and life experience are much more complicated and nuanced than that. For instance, while you might think I think the opposite from reading the above, I support capital punishment in some instances and think that the world is much larger and more complex than a purely mechanistic explanation can possibly convey. I am not unchanging, though, so these statements may mean nothing a year from now.

This blog is called the “Renaissance Millenial” for the simple reason that I am a millenial (sort of, kind of, depending on who you ask – I was born in 1983), and I cannot manage to devote myself to one thing. Instead, I’m more of a Renaissance man, focused on writing and role-playing as well as science, politics, religion, and other topics. I posed a question to my friends on what they liked about my writing, and they didn’t come to a consensus, so I decided to dedicate this blog to my diverse interests and to turn it into a platform for expressing those interests to you. With that in mind, I hope you’ll find it useful.